Large Oligomers Research Articles

Structural Basis of Oligomerization of N-Terminal Domain of Spider Aciniform Silk Protein.

Spider silk is self-assembled from water-soluble silk proteins through changes in the environment, including pH, salt concentrations, and shear force. The N-terminal domains of major and minor ampullate silk proteins have been found to play an important role in the assembly process through salt- and pH-dependent dimerization. Here, we identified the sequences of the N-terminal domains of aciniform silk protein (AcSpN) and major ampullate silk protein (MaSpN) from Nephila antipodiana (NA). Different from MaSpN, our biophysical characterization indicated that AcSpN assembles to form large oligomers, instead of a dimer, upon condition changes from neutral to acidic pH and/or from a high to low salt concentration. Our structural studies, by nuclear magnetic resonance spectroscopy and homology modelling, revealed that AcSpN and MaSpN monomers adopt similar overall structures, but have very different charge distributions contributing to the differential self-association features. The intermolecular interaction interfaces for AcSp oligomers were identified using hydrogen–deuterium exchange mass spectrometry and mutagenesis. On the basis of the monomeric structure and identified interfaces, the oligomeric structures of AcSpN were modelled. The structural information obtained will facilitate an understanding of silk fiber formation mechanisms for aciniform silk protein.

Recombinant Bri3 BRICHOS domain is a molecular chaperone with effect against amyloid formation and non-fibrillar protein aggregation

Molecular chaperones assist proteins in achieving a functional structure and prevent them from misfolding into aggregates, including disease-associated deposits. The BRICHOS domain from familial dementia associated protein Bri2 (or ITM2B) probably chaperones its specific proprotein region with high β-sheet propensity during biosynthesis. Recently, Bri2 BRICHOS activity was found to extend to other amyloidogenic, fibril forming peptides, in particular, Alzheimer’s disease associated amyloid-β peptide, as well as to amorphous aggregate forming proteins. However, the biological functions of the central nervous system specific homologue Bri3 BRICHOS are still to be elucidated. Here we give a detailed characterisation of the recombinant human (rh) Bri3 BRICHOS domain and compare its structural and functional properties with rh Bri2 BRICHOS. The results show that rh Bri3 BRICHOS forms more and larger oligomers, somewhat more efficiently prevents non-fibrillar protein aggregation, and less efficiently reduces Aβ42 fibril formation compared to rh Bri2 BRICHOS. This suggests that Bri2 and Bri3 BRICHOS have overlapping molecular mechanisms and that their apparently different tissue expression and processing may result in different physiological functions.

Percutaneous absorption of resveratrol and its oligomers to relieve psoriasiform lesions: In silico, in vitro and in vivo evaluations.

Resveratrol was shown to exert anti-inflammatory effects in experimental models of psoriasis. Several natural oligomers of resveratrol have been extracted from plants. We investigated the antipsoriatic activity of topical administration of resveratrol oligomers and explored the effect of the number of resveratrol subunits on skin absorption to establish the structure-permeation relationship (SPR). Three oligomers, ε-viniferin (dimer), ampelopsin C (trimer) and vitisin A (tetramer), extracted from Vitis thunbergii root were compared to the resveratrol glycoside polydatin. Delivery to porcine skin was assessed in vitro using the Franz cell. Keratinocytes activated with imiquimod (IMQ) were utilized to evaluate cytokine/chemokine inhibition. Topical application of resveratrol and oligomers was characterized in vivo by assessing cutaneous absorption, skin physiology, proinflammatory mediator expression, and histopathology in IMQ-treated mice. Skin deposition decreased as the molecular size and lipophilicity of the permeants increased. Resveratrol exhibited highest absorption, followed by ε-viniferin. The monomers resveratrol and polydatin exhibited higher flux across skin than the larger oligomers. In silico modeling revealed the permeants that strongly interacted with stratum corneum (SC) lipids exhibited lower transport to viable skin and the receptor compartment. In vitro, resveratrol and its derivatives had comparable ability to inhibit IMQ-induced IL-1β, IL-6, and CXCL8 secretion in activated keratinocytes. In vivo, topically applied ε-viniferin accumulated at higher levels than resveratrol (0.067 versus 0.029nmol/mg) in psoriasis-like mouse skin with impaired barrier capacity. Topical ε-viniferin alleviated psoriasiform symptoms and reduced IL-23 secretion (by 58% vs. 37%) more effectively than resveratrol. ε-Viniferin has potential as an anti-inflammatory agent to prevent or treat psoriasis.

Structure and activity of human surfactant protein D from different natural sources.

Surfactant protein D (SP-D) is a C-type lectin that participates in the innate immune defense of lungs. It binds pathogens through its carbohydrate recognition domain in a calcium-dependent manner. Human surfactant protein D (hSP-D) has been routinely obtained from bronchoalveolar lavage of patients suffering from pulmonary alveolar proteinosis (PAP) and from amniotic fluid (AF). As a consequence of the disease, hSP-D obtained from PAP is found in higher amounts and is mainly composed of higher order oligomeric forms. However, PAP-hSP-D has never been directly compared with nonpathological human protein in terms of structure and biological activity. Moreover, the quantitative distribution of the different hSP-D oligomeric forms in human protein obtained from a natural source has never been evaluated. In this work, we have determined the quantitative distribution of AF-hSP-D oligomers, characterized the sugars attached through the N-glycosylation site of the protein, and compared the activity of hSP-D from AF and PAP with respect to their ability to bind and agglutinate bacteria. We have found that fuzzy balls (40%) are the most abundant oligomeric form in AF-hSP-D, very closely followed by dodecamers (33%), with both together constituting 73% of the protein mass. The glycan attached to the N-glycosylation site was found to be composed of fucose, galactose, sialic acid, and N-acetylglucosamine. Finally, in the functional assays performed, hSP-D obtained from PAP showed higher potency, probably as a consequence of its higher proportion of large oligomers compared with hSP-D from AF.

Effect of additional hydroxy group on self-aggregation of synthetic zinc bacteriochlorophyll-c analogs

Zinc methyl 3-hydroxymethyl-pyropheophorbides-a possessing a hydroxymethyl or 2-hydroxyethyl group at the 20-position were prepared by chemical modification of naturally occurring chlorophyll-a. The synthetic bacterio-chlorophyll-c analog bearing the 201-hydroxy group self-aggregated in an aqueous Triton X-100 micellar solution to give large oligomers with red-shifted and broadened electronic absorption bands, which was similar to the chlorophyllous J-aggregates in the main light-harvesting antennas of green photosynthetic bacteria. By contrast, the other 202-hydroxylated analog did not aggregate under the same conditions to remain its monomeric species. The red shift in the longest wavelength (Qy) band by the self-aggregation of the former analog was greater than that of the corresponding 201-methyl substitute with a similar size (CH3 ≈ OH). These results could be ascribable to the less sterically demanding and more electron-withdrawing 20-hydroxymethyl group, compared with more interacting 2-hydroxyethyl and more electron-donating ethyl groups at the 20-position.

Sterically controlled and pH-dependent self-aggregation of synthetic zinc 3-(alkylamino)methylated chlorophyll-a derivatives in aqueous micellar solution

Zinc methyl 3-(methyl/ethylamino)methyl-pyropheophorbides-[Formula: see text] were prepared as models of photosynthetically active bacteriochlorophyll-[Formula: see text] possessing the 3[Formula: see text]-hydroxy group. The synthetic methylamino analog predominantly dimerized via two Zn[Formula: see text]N coordination bonds in aqueous Triton X-100 micelles, while the more sterically crowding and less coordinating ethylamino derivative self-aggregated to form large oligomers through single coordination and hydrogen bonds, Zn[Formula: see text]N–H[Formula: see text]O=C-13, similarly as in the natural self-aggregates of bacteriochlorophyll-[Formula: see text]. The artificial self-aggregates were dependent on the aqueous pH, but the dimer was less pH-sensitive and also more tolerant to the additional Triton X-100.

Stereoselective self-aggregation of zinc bacteriochlorophyll-d analogs possessing an O-substituted oxime moiety at the 13-position

Zinc methyl 3-hydroxymethyl-131-deoxo-pyropheophorbides-a possessing a variety of O-substituted oxime moieties at the 13-position were prepared as models of bacteriochlorophyll-d, which could be found in the main light-harvesting system of green photosynthetic bacteria by chemical modification of naturally occurring chlorophyll-a. The E/Z-stereoisomers of the synthetic O-substituted oximes were successfully separated by silica gel column chromatography. Most of these zinc bacteriochlorophyll-d analogs formed J-type self-aggregates in an aqueous Triton X-100 micelle solution, affording large oligomers whose Soret and Qy bands were red-shifted, compared with those of their monomers in tetrahydrofuran. The self-aggregation was dependent on their E/Z-stereochemistry. Thus, the E-stereoisomers showed the red-shifted electronic absorption bands, which were similar to those of the original bacteriochlorophyll-d bearing the 131-oxo group. On the other hand, the Z-stereoisomers exhibited the less red-shifted absorption bands than did the E-stereoisomers, to give different self-aggregates. In addition, the self-aggregation could be controlled by the size of the O-substituents in the oxime moiety.

Mutations in HspB1 and hereditary neuropathies.

Charcot-Marie-Tooth (CMT) disease is major hereditary neuropathy. CMT has been linked to mutations in a range of proteins, including the small heat shock protein HspB1. Here we review the properties of several HspB1 mutants associated with CMT. In vitro, mutations in the N-terminal domain lead to a formation of larger HspB1 oligomers when compared with the wild-type (WT) protein. These mutants are resistant to phosphorylation-induced dissociation and reveal lower chaperone-like activity than the WT on a range of model substrates. Mutations in the α-crystallin domain lead to the formation of yet larger HspB1 oligomers tending to dissociate at low protein concentration and having variable chaperone-like activity. Mutations in the conservative IPV motif within the C-terminal domain induce the formation of very large oligomers with low chaperone-like activity. Most mutants interact with a partner small heat shock protein, HspB6, in a manner different from that of the WT protein. The link between the altered physico-chemical properties and the pathological CMT phenotype is a subject of discussion. Certain HspB1 mutations appear to have an effect on cytoskeletal elements such as intermediate filaments and/or microtubules, and by this means damage the axonal transport. In addition, mutations of HspB1 can affect the metabolism in astroglia and indirectly modulate the viability of motor neurons. While the mechanisms of pathological mutations in HspB1 are likely to vary greatly across different mutations, further in vitro and in vivo studies are required for a better understanding of the CMT disease at molecular level.

Analysis of Oligomerization and Protein‐Protein Interactions within the Conjugation Machinery of Bacillus subtilis

Bacterial mating, or conjugation, is the transfer of DNA from one bacterial cell to another. Conjugation is significant to bacterial evolution and plays a large role in the spread of antibiotic resistance. The conjugation machinery of the Bacillus subtilis integrative and conjugative element ICEBs1 is a specialized DNA translocation channel known as a Type 4 Secretion System (T4SS). T4SSs are composed of multiple interacting oligomeric proteins that span the donor cell membrane. Previously, we found that the B. subtilis T4SS protein ConE (VirB4) interacts with itself and another T4SS protein, ConB (VirB8). These protein‐protein interactions were identified using a bacterial two hybrid method (BACTH) in which the proteins are fused to either the T18 or T25 domains of adenylate cyclase. Given that characterized VirB8 homologs oligomerize, we hypothesized that ConB interacts with itself, likely forming trimers or larger oligomers. To test this hypothesis, the conB gene was amplified by PCR and ligated into vectors that encode either the T18 or T25 domains. The plasmids were transformed into Escherichia coli and verified by sequencing. Subsequent BACTH assays in which the plasmids were co‐transformed into E. coli cells verified the interaction between T25‐ConB and T18‐ConB. We have performed site‐directed mutagenesis on the conB gene and intend to determine which domains of ConB are required for oligomerization and for interaction with ConE. Our work should provide greater insight into the structure and function of the T4SSs of B. subtilis and other Gram‐positive bacteria.

BciC-Catalyzed C132 -Demethoxycarbonylation of Metal Pheophorbide a Alkyl Esters.

Bacteriochlorophyll c molecules self-aggregate to form large oligomers in the core part of chlorosomes, which are the main light-harvesting antenna systems of green photosynthetic bacteria. In the biosynthetic pathway of bacteriochlorophyll c, a BciC enzyme catalyzes the removal of the C132 -methoxycarbonyl group of chlorophyllide a, which possesses a free propionate residue at the C17-position and a magnesium ion as the central metal. The in vitro C132 -demethoxycarbonylations of chlorophyll a derivatives with various alkyl propionate residues and central metals were examined by using the BciC enzyme derived from one green sulfur bacteria species, Chlorobaculum tepidum. The BciC enzymatic reactions of zinc pheophorbide a alkyl esters were gradually suppressed with an increase of the alkyl chain length in the C17-propionate residue (from methyl to pentyl esters) and finally the hexyl ester became inactive for the BciC reaction. Although not only the zinc but also nickel and copper complexes were demethoxycarbonylated by the BciC enzyme, the reactions were largely dependent on the coordination ability of the central metals: Zn>Ni>Cu. The above substrate specificity indicates that the BciC enzyme would not bind directly to the carboxy group of chlorophyllide a, but would bind to its central magnesium to form the stereospecific complex of BciC with chlorophyllide a, giving pyrochlorophyllide a, which lacks the (132 R)-methoxycarbonyl group.

Mitochondrial residence of the apoptosis inducer BAX is more important than BAX oligomerization in promoting membrane permeabilization

Permeabilization of the mitochondrial outer membrane is a key step in the intrinsic apoptosis pathway, triggered by the release of mitochondrial intermembrane space proteins into the cytoplasm. The BCL-2-associated X apoptosis regulator (BAX) protein critically contributes to this process by forming pores in the mitochondrial outer membrane. However, the relative roles of the mitochondrial residence of BAX and its oligomerization in promoting membrane permeabilization are unclear. To this end, using both cell-free and cellular experimental systems, including membrane permeabilization, size-exclusion chromatography-based oligomer, and retrotranslocation assays, along with confocal microscopy analysis, here we studied two BAX C-terminal variants, T182I and G179P. Neither variant formed large oligomers when activated in liposomes. Nevertheless, the G179P variant could permeabilize liposome membranes, suggesting that large BAX oligomers are not essential for the permeabilization. However, when G179P was transduced into BAX/BCL2 agonist killer (BAK) double-knockout mouse embryonic fibroblasts, its location was solely cytoplasmic, and it then failed to mediate cell death. In contrast, T182I was inefficient in both liposome insertion and permeabilization. Yet, when transduced into cells, BAXT182I resided predominantly on mitochondria, because of its slow retrotranslocation and mediated apoptosis as efficiently as WT BAX. We conclude that BAX's mitochondrial residence in vivo, regulated by both targeting and retrotranslocation, is more significant for its pro-apoptotic activity than its ability to insert and to form higher-order oligomers in model membranes. We propose that this finding should be taken into account when developing drugs that modulate BAX activity.

Dynamin PH Domain Interactions with Phosphatidylinositol Lipids in Membrane

During the final stages of endocytosis, large scale dynamin protein oligomers are formed around lipid vesicle necks to cause membrane fission. The interaction of dynamin with the lipid membrane is controlled by the PH domain of the protein. PH domains are found in many proteins and tend to bind with phosphatidylinositol lipids(PIP2) in membranes. Molecular dynamics simulations were used to study the interaction of the PH domain with membranes during fission. The interactions between the curvature sensing loops on the PH domain with the membrane are also of particular interest. In these studies, we varied the composition of the lipid membranes to understand the effect of PIP2 concentration and negative lipid charge. The PH domain was then simulated in contact with the membrane to determine what interactions occur. These simulations will help shed light on the role of the PH domain in modulating the binding of dynamin to the lipid membrane, a key step in dynamin induced fission.

Identification and characterization of self-association domains on small ankyrin 1 isoforms

In striated muscles, the large scaffolding protein obscurin and a small SR-integral membrane protein sAnk1.5 control the retention of longitudinal SR across the sarcomere. How a complex of these proteins facilitates localization of longitudinal SR has yet to be resolved, but we hypothesize that obscurin interacts with a complex of sAnk1.5 proteins. To begin to address this hypothesis, we demonstrate that sAnk1.5 interacts with itself and identify two domains mediating self-association. Specifically, we show by co-precipitation and FLIM-FRET analysis that sAnk1.5 and another small AnkR isoform (sAnk1.6) interact with themselves and each other. We demonstrate that obscurin interacts with a complex of sAnk1.5 proteins and that this complex formation is enhanced by obscurin-binding. Using FLIM-FRET analysis, we show that obscurin interacts with sAnk1.5 alone and with sAnk1.6 in the presence of sAnk1.5. We find that sAnk1.5 self-association is disrupted by mutagenesis of residues Arg64-Arg69, residues previously associated with obscurin-binding. Molecular modeling of two interacting sAnk1.5 monomers facilitated the identification of Gly31-Val36 as an additional site of interaction, which was subsequently corroborated by co-precipitation and FLIM-FRET analysis. In closing, these results support a model in which sAnk1.5 forms large oligomers that interact with obscurin to facilitate the retention of longitudinal SR throughout skeletal and cardiac myocytes.

High-resolution probing of early events in amyloid-β aggregation related to Alzheimer's disease.

In Alzheimer's disease (AD), soluble oligomers of amyloid-β (Aβ) are emerging as a crucial entity in driving disease progression as compared to insoluble amyloid deposits. The lacuna in establishing the structure to function relationship for Aβ oligomers prevents the development of an effective treatment for AD. While the transient and heterogeneous properties of Aβ oligomers impose many challenges for structural investigation, an effective use of a combination of NMR techniques has successfully identified and characterized them at atomic-resolution. Here, we review the successful utilization of solution and solid-state NMR techniques to probe the aggregation and structures of small and large oligomers of Aβ. Biophysical studies utilizing the commonly used solution and 19F based NMR experiments to identify the formation of small size early intermediates and to obtain their structures, and dock-lock mechanism of fiber growth at atomic-resolution are discussed. In addition, the use of proton-detected magic angle spinning (MAS) solid-state NMR experiments to obtain high-resolution insights into the aggregation pathways and structures of large oligomers and other aggregates is also presented. We expect these NMR based studies to be valuable for real-time monitoring of the depletion of monomers and the formation of toxic oligomers and high-order aggregates under a variety of conditions, and to solve the high-resolution structures of small and large size oligomers for most amyloid proteins, and therefore to develop inhibitors and drugs.

Non-catalytic oxidative depolymerization of lignin in perfluorodecalin to produce phenolic monomers

Increasing the selectivity of lignin oxidation toward phenolic monomers by enhancing oxygen mass transfer using perfluorocarbon media.

The structure of the endogenous ESX-3 secretion system.

The ESX (or Type VII) secretion systems are protein export systems in mycobacteria and many Gram-positive bacteria that mediate a broad range of functions including virulence, conjugation, and metabolic regulation. These systems translocate folded dimers of WXG100-superfamily protein substrates across the cytoplasmic membrane. We report the cryo-electron microscopy structure of an ESX-3 system, purified using an epitope tag inserted with recombineering into the chromosome of the model organism Mycobacterium smegmatis. The structure reveals a stacked architecture that extends above and below the inner membrane of the bacterium. The ESX-3 protomer complex is assembled from a single copy of the EccB3, EccC3, and EccE3 and two copies of the EccD3 protein. In the structure, the protomers form a stable dimer that is consistent with assembly into a larger oligomer. The ESX-3 structure provides a framework for further study of these important bacterial transporters.

The Mitochondrial Small Heat Shock Protein HSP22 from Pea is a Thermosoluble Chaperone Prone to Co-Precipitate with Unfolding Client Proteins.

The small heat shock proteins (sHSPs) are molecular chaperones that share an alpha-crystallin domain but display a high diversity of sequence, expression, and localization. They are especially prominent in plants, populating most cellular compartments. In pea, mitochondrial HSP22 is induced by heat or oxidative stress in leaves but also strongly accumulates during seed development. The molecular function of HSP22 was addressed by studying the effect of temperature on its structural properties and chaperone effects using a recombinant or native protein. Overexpression of HSP22 significantly increased bacterial thermotolerance. The secondary structure of the recombinant protein was not affected by temperature in contrast with its quaternary structure. The purified protein formed large polydisperse oligomers that dissociated upon heating (42 °C) into smaller species (mainly monomers). The recombinant protein appeared thermosoluble but precipitated with thermosensitive proteins upon heat stress in assays either with single protein clients or within complex extracts. As shown by in vitro protection assays, HSP22 at high molar ratio could partly prevent the heat aggregation of rhodanese but not of malate dehydrogenase. HSP22 appears as a holdase that could possibly prevent the aggregation of some proteins while co-precipitating with others to facilitate their subsequent refolding by disaggregases or clearance by proteases.

Oligomerization of RIG-I and MDA5 2CARD domains.

The innate immune system is the first line of defense against invading pathogens. The retinoic acid-inducible gene I (RIG-I) like receptors (RLRs), RIG-I and melanoma differentiation-associated protein 5 (MDA5), are critical for host recognition of viral RNAs. These receptors contain a pair of N-terminal tandem caspase activation and recruitment domains (2CARD), an SF2 helicase core domain, and a C-terminal regulatory domain. Upon RLR activation, 2CARD associates with the CARD domain of MAVS, leading to the oligomerization of MAVS, downstream signaling and interferon induction. Unanchored K63-linked polyubiquitin chains (polyUb) interacts with the 2CARD domain, and in the case of RIG-I, induce tetramer formation. However, the nature of the MDA5 2CARD signaling complex is not known. We have used sedimentation velocity analytical ultracentrifugation to compare MDA5 2CARD and RIG-I 2CARD binding to polyUb and to characterize the assembly of MDA5 2CARD oligomers in the absence of polyUb. Multi-signal sedimentation velocity analysis indicates that Ub4 binds to RIG-I 2CARD with a 3:4 stoichiometry and cooperatively induces formation of an RIG-I 2CARD tetramer. In contrast, Ub4 and Ub7 interact with MDA5 2CARD weakly and form complexes with 1:1 and 2:1 stoichiometries but do not induce 2CARD oligomerization. In the absence of polyUb, MDA5 2CARD self-associates to forms large oligomers in a concentration-dependent manner. Thus, RIG-I and MDA5 2CARD assembly processes are distinct. MDA5 2CARD concentration-dependent self-association, rather than polyUb binding, drives oligomerization and MDA5 2CARD forms oligomers larger than tetramer. We propose a mechanism where MDA5 2CARD oligomers, rather than a stable tetramer, function to nucleate MAVS polymerization.

Aggregation Patterns in Low- and High-Charge Anions Define Opposite Solubility Trends.

Molecular dynamics simulations in aqueous solution reveal the existence of two distinct patterns of aggregation in low and high charge density Lindqvist-type polyoxometalates (POMs). Our results indicate the presence of contact and solvent-shared ion pairs and specific and preferential interactions of alkalis with POMs. Highly charged POMs are capable of breaking apart the Li+ and Cs+ solvation shell, thus enhancing the formation of long-lived alkali-POM contact ion pairs, where alkalis act as an electrostatic "glue" forming large oligomers. Stronger ion pair interactions for Li+ than for Cs+ promote lower solubility for Li+ than for Cs+, evoking anomalous solubility trends. Lower charge density POMs are not capable of disrupting the Li+ solvation shell and only solvent-shared ion pairs are formed, whereas for Cs+, contact ion pairs exist. The large number of oxygen atoms in the POM surface enhances the hydrogen bonds between POM and water, thus promoting aggregation. In this case, aggregation follows normal solubility trends. Thus, aggregation depends on the strength of ion pair interactions, the capacity of POM to disrupt alkali's solvation shell, and the contact surface area between the solvent and POM.

Theoretical Studies of Structures and Conformational Analysis of Anthracene-2,7-diyl Cyclic Oligomers

Abstract The structures and conformation of anthracene-2,7-diyl cyclic oligomers were investigated by DFT calculations. The energy minimum and transition state structures of the oligomers ranging from pentamer to nonamer were optimized at the M05-2X/6-31G(d) level. The mechanisms of conformational interconversion were analyzed on the basis of the calculated structures and the thermodynamic energies. The number of structures and the conformational flexibility rapidly increased with increasing ring size. In the stable structures, the dihedral angles between the anthracene units were ca. ±40° or ±140°, and the obtuse angles appeared only in large oligomers. We estimated the cavity size of the cyclic oligomers from the calculated structures and their strain energies by thermochemical calculations of the homodesmotic reactions.